Cyprus has threatened to block Turkey's EU membership talks unless Ankara lifts its trade restrictions on Nicosia.
Turkey's bid has polarised opinion in Europe
The European Commission on Wednesday recommended that some elements of the talks with Turkey should be frozen until Ankara opens its ports to Cyprus.
A Cypriot government spokesman said the talks could be vetoed if Nicosia was unhappy with a decision on the issue to be taken at an EU summit in December.
Turkey's refusal to recognise Cyprus is a key obstacle to its membership bid.
The European Commission recommended that eight of the 35 areas of negotiation between the EU and Turkey should be suspended.
EU foreign ministers are due to decide on 11 December at the summit in Brussels whether to back the proposal, with European Commission president saying he expected the measure would be approved.
But Cypriot government spokesman Christodoulos Pashiardis said: "If we are not satisfied with the EU conclusions, we will register our disagreement and the conclusions will not be valid.
"In such a case, we will revert and exercise our right not to permit the opening of chapters of Turkey's accession course," he said.
Cypriot President Tassos Papadopoulos said earlier the European Commission recommendation was too soft.
"We believe it does not offer any form of pressure on Turkey to comply with its obligations.. This is not helpful at all," he said.
On Wednesday, Turkish television channels quoted Prime Minister Tayyip Erdogan as saying the recommendation was "unacceptable".
Ankara also said it was determined to press on with the accession talks it began in October last year.
Turkey's chief negotiator with the EU, Ali Babacan, suggested that the Cyprus issue should be left out of the talks.
"We oppose the linkage between the negotiations and Cyprus," Mr Babacan told the Financial Times newspaper.
The EU insists that Turkey fulfil its commitment to open its ports to traffic from Cyprus, but Turkey says it will not do so until the EU eases its embargo on Turkish-controlled northern Cyprus.
Suspending some chapters would not mean Turkey's application would be halted altogether, but could make it difficult to get full negotiations back on track, BBC's Jonny Dymond in Brussels says.
Finnish Prime Minister Matti Vanhanen will visit Turkey on Friday to meet Mr Erdogan, in a last-ditch effort to reach a breakthrough.
Cyprus has been divided since 1974, when Turkish troops invaded to counter a Greek Cypriot coup backed by the military junta ruling Greece at the time.